Abstract
BackgroundSmall RNA molecules play important roles in many biological processes and their dysregulation or dysfunction can cause disease. The current method of choice for genome-wide sRNA expression profiling is deep sequencing.ResultsHere we present Oasis 2, which is a new main release of the Oasis web application for the detection, differential expression, and classification of small RNAs in deep sequencing data. Compared to its predecessor Oasis, Oasis 2 features a novel and speed-optimized sRNA detection module that supports the identification of small RNAs in any organism with higher accuracy. Next to the improved detection of small RNAs in a target organism, the software now also recognizes potential cross-species miRNAs and viral and bacterial sRNAs in infected samples. In addition, novel miRNAs can now be queried and visualized interactively, providing essential information for over 700 high-quality miRNA predictions across 14 organisms. Robust biomarker signatures can now be obtained using the novel enhanced classification module.ConclusionsOasis 2 enables biologists and medical researchers to rapidly analyze and query small RNA deep sequencing data with improved precision, recall, and speed, in an interactive and user-friendly environment.Availability and ImplementationOasis 2 is implemented in Java, J2EE, mysql, Python, R, PHP and JavaScript. It is freely available at https://oasis.dzne.de
Highlights
Small RNA molecules play important roles in many biological processes and their dysregulation or dysfunction can cause disease
Recent additions to sRNA analysis web applications include omiRas [11], supporting quantification, differential expression and interactive network visualization; mirTools 2.0 [20] that allows for differential expression and gene ontology analysis of detected sRNAs; MAGI, an all-in-one workflow with detailed interactive web reports [8]; Chimira that allows for the detection of miRNA edits and modifications [17]; sRNAtoolbox [15] performs expression profiling of sRNA-seq data, differential expression as well as target gene prediction and visualization of analysis results; and Oasis [2], which supports the detection and annotation of known and Rahman et al BMC Bioinformatics (2018) 19:54 novel sRNAs, multivariate differential expression analysis, biomarker detection, and job automation via an advanced programming interface (API)
When tested on four publically available datasets, Oasis 2 detected 19 out of 27 (70%) differentially expressed (DE) genes that were previously validated and did not detect 4/4 (100%) miRNAs that showed a significant DE in deep sequencing but could not be validated with qPCR, highlighting both the sensitivity and specificity of Oasis 2
Summary
We compared the set of analysis options and the analysis speed of Oasis 2 to six state-of-the-art sRNA analysis web applications, including Oasis, omiRas, mirTools 2.0,. Pathogen detection and sample classification To assess the performance of the pathogen detection we analyzed 5 datasets with known viral or bacterial infections (Additional file 1: Table S6). To benchmark the improved classification routine, we compared the performance of the old Oasis classification module (unbalanced sampling with all variables) to the new Oasis 2 classification module using balanced sampling and feature optimization using three demo datasets (see Detection and Differential Expression of sRNAs and Additional file 1: Figure S2). Runtime estimates We estimated the runtime of Oasis 2 using the above-mentioned AD, Psoriasis, and Renal cancer datasets and compared the results to runtime estimates for omiRas, mirTools 2.0, MAGI, Chimira and sRNAtoolbox, five recently developed web applications for the analysis of sRNA-seq data (Table 3, Additional file 1: Table S7). Oasis 2 is the fastest of the state-of-the-art web applications we could compare to and has no restrictions on the sample number or size
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